diff --git a/docs/releases/v2.14.5.md b/docs/releases/v2.14.5.md
index 243ce4cf33361cdd240846c1b922bb61666e3921..8ebec4a4287fd3b225e23e2a906f83a8e30cd5e0 100644
--- a/docs/releases/v2.14.5.md
+++ b/docs/releases/v2.14.5.md
@@ -10,7 +10,8 @@
- Added legend to region hierarchy
- Allow latest queried concept in feature view
- Allow experimental flag to be set to be on at runtime (this also shows the button, allow toggling of experimental features)
-- Added code snippet to limited panels
+- Feature: added supported for .annot fsaverage label
+- (experimental) Added code snippet to limited panels
- (experimental) allow addition of custom linear coordinate space
- (experimental) show BigBrain slice number
diff --git a/src/atlasComponents/sapi/translateV3.ts b/src/atlasComponents/sapi/translateV3.ts
index 03659664a737629229c78ae3a5e6c04c1660fd06..b0eb95d8be166dd449c86cadb2662bc2964749d9 100644
--- a/src/atlasComponents/sapi/translateV3.ts
+++ b/src/atlasComponents/sapi/translateV3.ts
@@ -398,13 +398,19 @@ class TranslateV3 {
}
async translateLabelledMapToThreeLabel(map:PathReturn<"/map">) {
- const threeLabelMap: Record<string, { laterality: 'left' | 'right', url: string, region: LabelledMap[] }> = {}
- const registerLayer = (url: string, laterality: 'left' | 'right', region: string, label: number) => {
+ const threeLabelMap: Record<string, {
+ laterality: 'left' | 'right'
+ url: string
+ region: LabelledMap[]
+ clType: 'baselayer/threesurfer-label/gii-label' | 'baselayer/threesurfer-label/annot'
+ }> = {}
+ const registerLayer = (url: string, clType: 'baselayer/threesurfer-label/gii-label' | 'baselayer/threesurfer-label/annot', laterality: 'left' | 'right', region: string, label: number) => {
if (!threeLabelMap[url]) {
threeLabelMap[url] = {
laterality,
region: [],
url,
+ clType
}
}
@@ -416,18 +422,26 @@ class TranslateV3 {
for (const regionname in map.indices) {
for (const { volume: volIdx, fragment, label } of map.indices[regionname]) {
const volume = map.volumes[volIdx || 0]
- if (!volume.formats.includes("gii-label")) {
- // Does not support gii-label... skipping!
- continue
+ let clType: 'baselayer/threesurfer-label/gii-label' | 'baselayer/threesurfer-label/annot' | null = null
+ let providedVolume: typeof volume['providedVolumes'][string] | null = null
+ if (volume.formats.includes("gii-label")) {
+ clType = 'baselayer/threesurfer-label/gii-label'
+ providedVolume = volume.providedVolumes["gii-label"]
+ }
+ if (volume.formats.includes("freesurfer-annot")) {
+ clType = 'baselayer/threesurfer-label/annot'
+ providedVolume = volume.providedVolumes["freesurfer-annot"]
}
- const { ["gii-label"]: giiLabel } = volume.providedVolumes
-
+ if (!providedVolume || !clType) {
+ // does not support baselayer threesurfer label, skipping
+ continue
+ }
if (!fragment || !["left hemisphere", "right hemisphere"].includes(fragment)) {
console.warn(`either fragment not defined, or fragment is not '{left|right} hemisphere'. Skipping!`)
continue
}
- if (!giiLabel[fragment]) {
+ if (!providedVolume[fragment]) {
// Does not support gii-label... skipping!
continue
}
@@ -438,7 +452,7 @@ class TranslateV3 {
console.warn(`cannot determine the laterality! skipping`)
continue
}
- registerLayer(giiLabel[fragment], laterality, regionname, label)
+ registerLayer(providedVolume[fragment], clType, laterality, regionname, label)
}
}
return threeLabelMap
diff --git a/src/index.html b/src/index.html
index 3d3708ae31b94d2ecca8c544cc467f841e621e6b..8158adec9af469dbf1fccc909f49c26ed7e297dc 100644
--- a/src/index.html
+++ b/src/index.html
@@ -12,7 +12,7 @@
<link rel="stylesheet" href="version.css">
<link rel="icon" type="image/png" href="assets/favicons/favicon-128-light.png"/>
<script src="extra_js.js"></script>
- <script src="https://unpkg.com/three-surfer@0.0.13/dist/bundle.js" defer></script>
+ <script src="https://unpkg.com/three-surfer@0.0.15/dist/bundle.js" defer></script>
<script type="module" src="https://unpkg.com/ng-layer-tune@0.0.26/dist/ng-layer-tune/ng-layer-tune.esm.js"></script>
<script src="https://cdn.plot.ly/plotly-2.24.1.min.js" charset="utf-8"></script>
<title>Siibra Explorer</title>
diff --git a/src/state/atlasAppearance/const.ts b/src/state/atlasAppearance/const.ts
index ed44978229e5f957ea50d0c7764e6fcb545fab6a..16195d9e3392acfc46c6a172504c5eaa0d6dfaf3 100644
--- a/src/state/atlasAppearance/const.ts
+++ b/src/state/atlasAppearance/const.ts
@@ -22,7 +22,7 @@ export type ThreeSurferCustomLayer = {
} & CustomLayerBase
export type ThreeSurferCustomLabelLayer = {
- clType: 'baselayer/threesurfer-label'
+ clType: 'baselayer/threesurfer-label/gii-label' | 'baselayer/threesurfer-label/annot'
source: string
laterality: 'left' | 'right'
} & CustomLayerBase
diff --git a/src/viewerModule/threeSurfer/store/effects.ts b/src/viewerModule/threeSurfer/store/effects.ts
index 86992a1c3330ed1b3150467d04aa4f984cde169e..7eef500a7653419655e9d384edd2c6f50b87262c 100644
--- a/src/viewerModule/threeSurfer/store/effects.ts
+++ b/src/viewerModule/threeSurfer/store/effects.ts
@@ -43,7 +43,8 @@ export class ThreeSurferEffects {
map(
cl => cl.filter(layer =>
layer.clType === "baselayer/threesurfer" ||
- layer.clType === "baselayer/threesurfer-label"
+ layer.clType === "baselayer/threesurfer-label/annot" ||
+ layer.clType === "baselayer/threesurfer-label/gii-label"
) as ThreeSurferCustomLayer[]
)
)
@@ -121,9 +122,9 @@ export class ThreeSurferEffects {
switchMap(({ labels }) => {
const labelMaps: ThreeSurferCustomLabelLayer[] = []
for (const key in labels) {
- const { laterality, url } = labels[key]
+ const { laterality, url, clType } = labels[key]
labelMaps.push({
- clType: 'baselayer/threesurfer-label',
+ clType,
id: `${url}-${laterality}`,
laterality,
source: url
diff --git a/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts b/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts
index 4a5c1238064d88be6953b2e65411e7c00e25862d..74d86122db39c3c39af97b85165d55e2b5cdfa56 100644
--- a/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts
+++ b/src/viewerModule/threeSurfer/threeSurferGlue/threeSurfer.component.ts
@@ -1,6 +1,6 @@
import { Component, Output, EventEmitter, ElementRef, OnDestroy, AfterViewInit, Optional, ChangeDetectionStrategy } from "@angular/core";
import { EnumViewerEvt, IViewer, TViewerEvent } from "src/viewerModule/viewer.interface";
-import { BehaviorSubject, combineLatest, concat, forkJoin, from, merge, NEVER, Observable, of, Subject } from "rxjs";
+import { BehaviorSubject, combineLatest, concat, forkJoin, from, merge, NEVER, Observable, of, Subject, throwError } from "rxjs";
import { catchError, debounceTime, distinctUntilChanged, filter, map, scan, shareReplay, startWith, switchMap, tap, withLatestFrom } from "rxjs/operators";
import { ComponentStore, LockError } from "src/viewerModule/componentStore";
import { select, Store } from "@ngrx/store";
@@ -95,6 +95,17 @@ type TThreeSurfer = {
loadColormap: (url: string) => Promise<GiiInstance>
setupAnimation: () => void
dispose: () => void
+ loadVertexData: (url: string) => Promise<{
+ vertex: number[]
+ labels: {
+ index: number
+ name: string
+ color: number[]
+ vertices: number[]
+ }[]
+ readonly vertexLabels: Uint16Array
+ readonly colormap: Map<number, number[]>
+ }>
control: any
camera: any
customColormap: WeakMap<TThreeGeometry, any>
@@ -252,7 +263,9 @@ export class ThreeSurferGlueCmp implements IViewer<'threeSurfer'>, AfterViewInit
)
private vertexIndexLayers$: Observable<ThreeSurferCustomLabelLayer[]> = this.customLayers$.pipe(
- map(layers => layers.filter(l => l.clType === "baselayer/threesurfer-label") as ThreeSurferCustomLabelLayer[]),
+ map(layers => layers.filter(l =>
+ l.clType === "baselayer/threesurfer-label/gii-label" || l.clType === "baselayer/threesurfer-label/annot"
+ ) as ThreeSurferCustomLabelLayer[]),
distinctUntilChanged(arrayEqual((o, n) => o.id === n.id)),
)
@@ -265,22 +278,37 @@ export class ThreeSurferGlueCmp implements IViewer<'threeSurfer'>, AfterViewInit
),
switchMap(layers =>
forkJoin(
- layers.map(layer =>
- from(
- this.tsRef.loadColormap(layer.source)
- ).pipe(
- map(giiInstance => {
- let vertexIndices: number[] = giiInstance[0].getData()
- if (giiInstance[0].attributes.DataType === 'NIFTI_TYPE_INT16') {
- vertexIndices = (window as any).ThreeSurfer.GiftiBase.castF32UInt16(vertexIndices)
- }
- return {
- indexLayer: layer,
- vertexIndices
- }
- })
- )
- )
+ layers.map(layer => {
+ if (layer.clType === "baselayer/threesurfer-label/gii-label") {
+ return from(
+ this.tsRef.loadColormap(layer.source)
+ ).pipe(
+ map(giiInstance => {
+ let vertexIndices: number[] = giiInstance[0].getData()
+ if (giiInstance[0].attributes.DataType === 'NIFTI_TYPE_INT16') {
+ vertexIndices = (window as any).ThreeSurfer.GiftiBase.castF32UInt16(vertexIndices)
+ }
+ return {
+ indexLayer: layer,
+ vertexIndices
+ }
+ })
+ )
+ }
+ if (layer.clType === "baselayer/threesurfer-label/annot") {
+ return from(
+ this.tsRef.loadVertexData(layer.source)
+ ).pipe(
+ map(v => {
+ return {
+ indexLayer: layer,
+ vertexIndices: v.vertexLabels
+ }
+ })
+ )
+ }
+ return throwError(() => new Error(`layer is neither annot nor gii-label`))
+ })
)
),
map(layers => {
@@ -317,8 +345,13 @@ export class ThreeSurferGlueCmp implements IViewer<'threeSurfer'>, AfterViewInit
const { label, region } = curr
let key : 'left' | 'right'
- if ( /left/i.test(region.name) ) key = 'left'
- if ( /right/i.test(region.name) ) key = 'right'
+ if (
+ /left/i.test(region.name) || /^lh/i.test(region.name)
+ ) key = 'left'
+ if (
+ /right/i.test(region.name) || /^rh/i.test(region.name)
+ ) key = 'right'
+
if (!key) {
/**
* TODO